similar to: weird bug with parallel, RSQlite and tcltk

On Wed, 17 May 2023 13:55:59 +0000 akshay kulkarni <akshay_e4 at hotmail.com> wrote: > So that means mclapply should run properly, i.e output a try class > object and exit. But it didn't. Can you shed some light on why this > happened? What's your sessionInfo()? Are you using a GUI frontend? mclapply() relies on the fork() system call, which is tricky to get right in a

On Fri, 9 Jun 2023 18:01:44 +0000 akshay kulkarni <akshay_e4 at hotmail.com> wrote: > > LYG <- pbmclapply(LYGH,FUN = arfima,mc.cores = 2,mc.preschedule = > > FALSE) > | > | > 0%, ETA NA^ > > It just hangs. My questions from the last time still stand: 0) What is your

Dear all, Consider this code: >library("data.table") >unloadNamespace('data.table') It produces some warnings Warning in FUN(X[[1L]], ...) : Created a package name, ‘2013-10-29 17:05:51’, when none found Warning in FUN(X[[1L]], ...) : Created a package name, ‘2013-10-29 17:05:51’, when none found ... The warning is produced by the getPackageName() function. e.g.

The following program is whittled down from a much larger program that always works on Intel, and always works on AMD's threadripper with lapply but not mclappy. With mclapply on AMD, all processes go into "suspend" mode and the program then hangs. This bug is replicable on an AMD Ryzen Threadripper 2950X 16-Core Processor (128GB RAM), running latest ubuntu 18.04. The R version

Dear all, I got an issue trying to parse excel files in parallel using XLConnect, the process hangs forever. Martin Studer, the maintainer of XLConnect kindly investigated the issue, identified rJava as a possible cause of the problem: This does not work (hangs): library(parallel) require(rJava) .jinit() res <- mclapply(1:2, function(i) {

Hello, I have a package with a namespace. Because I use Roxygen that overwrites the NAMESPACE file each time it is run, I use a R/zzz.R file with an .onLoad() and .onUnload() functions to take care of loading and unloading my shared library. The problem: if I load my library from a local directory, then the unloading of the package fails, e.g: # loads fine >library(Foo,

Dear Jeff, There was a problem in LYGH and lapply threw an error, but mclapply got stuck in an infinite loop. The doc for mclapply says that mclapply runs under try() with silent = TRUE. So that means mclapply should run properly, i.e output a try class object and exit. But it didn't. Can you shed some light on why this happened? THanking you, Yours sincerely, AKSHAY M

Dear members, I am using pbmcapply to parellise my code. But the following code doesn't work: > LYG <- pbmclapply(LYGH,FUN = arfima,mc.cores = 2,mc.preschedule = FALSE) | | 0%, ETA NA^ It just hangs. But the

Hello, Consider this: 1) library(parallel) res <- mclapply(1:2, stop) #Warning message: #In mclapply(1:2, stop) : # all scheduled cores encountered errors in user code is(res[[1]], 'try-error') #[1] FALSE 2) library(parallel) res <- mclapply(1:2, stop, mc.preschedule=FALSE) #Warning message: #In mclapply(1:2, stop, mc.preschedule = FALSE) : # 2 function calls resulted in an

Dear all I want to convert a apply to lapply. The reason for that is that there is a function mclappy that uses exact the same format as the lapply function. My code looks like that mean_power_per_tip <- function(data) {         return((apply(data[,],2,MeanTip))); } where data is a [m,n] matrix. I would like to thank you in advance for your help B.R Alex [[alternative HTML version

Hi Inaki, > "Performant"... in terms of what. If the cost of copying the data > predominates over the computation time, maybe you didn't need > parallelization in the first place. Performant in terms of speed. There's no copying in that example using `mclapply` and so it is significantly faster than other alternatives. It is a very simple and contrived example, but

Thanks for all your great answers. The app I?m working on is indeed an exploratory data analysis tool for gene expression, which requires a bunch of bioconductor packages. I guess for now, my best solution is to divide my app into modules and load/unload packages as the user switch from one module to another. This brought me another question: it seems that unload package with the

Dear Ivan, REgrets to reply this late... By "holding a lock", you mean a bug in the process right (I am not a computer science guy, excuse my naivete)? THanking you, Yours sincerely, AKSHAY M KULKARNI ________________________________ From: Ivan Krylov <krylov.r00t at gmail.com> Sent: Thursday, May 18, 2023 1:08 PM To: akshay kulkarni <akshay_e4 at

Dear All, Since upgrading to 3.6.0, I've been getting a strange error messages from the child process when using mcparallel/mccollect. Before filing a report in the Bugzilla, I want to figure out whether I had been doing something wrong all this time and R 3.6.0 has exposed it, or whether something else is going on. # Background # Ultimately, what I want to do is to be able to set a time

I have recently installed R on DEC Alpha OSF 5.1. The first regression test (reg-test-1.R) failed with an unresolved symbol in lapack.so: 2246839:/data/h1/bifdev/apps/wga/R-1.9.1/bin/R.bin: /sbin/loader: Fatal Error: call to unresolved symbol from /data/h1/bifdev/apps/wga/R-1.9.1/modules/lapack.so (pc=0x3ffbfe22b60) Further investigation has revealed that there is NO problem with lapack.so. The

I have recently installed R on DEC Alpha OSF 5.1. The first regression test (reg-test-1.R) failed with an unresolved symbol in lapack.so: 2246839:/data/h1/bifdev/apps/wga/R-1.9.1/bin/R.bin: /sbin/loader: Fatal Error: call to unresolved symbol from /data/h1/bifdev/apps/wga/R-1.9.1/modules/lapack.so (pc=0x3ffbfe22b60) Further investigation has revealed that there is NO problem with lapack.so. The

On Feb 5, 2010, at 10:04 AM, Markus Loecher wrote: > Hi Simon, > I recently switched to a different flavor of Linux and find that the children that are spawn off by e.g. mclapply() seem to persist forever until I kill them explicitly. > Is there anything I can do ? > I can reproduce the issue on Debian amd64 Linux and it seems that for some reason an additional wait() is necessary

In the documentation the closed thing I see to an explanation of this is that ?detach says "Unloading some namespaces has undesirable side effects" Can anyone explain why unloading tseries will load zoo? I don't think this behavior is specific to tseries, it's just an example. I realize one would not usually unload something that is not loaded, but I would expect it to do

Hello, I apologized if this had already been addressed, and I also submitted this problem on SO: http://stackoverflow.com/questions/20268021/how-to-catch-warnings-sent-during-s4-method-selection Example code: setGeneric('my_method', function(x) standardGeneric('my_method') ) setMethod('my_method', 'ANY', function(x) invisible())

RSQLite.extfuns provides SQLite extension functions for use with RSQLite. The package is a wrapper of extension functions written by Liam Healy and made available through the SQLite website (http://www.sqlite.org/contrib). You can make the extension functions available on a per db connection basis like this: library("RSQLite.extfuns") db <- dbConnect(SQLite(), dbname =